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Summary

Bio::LiveSeq::DNA - DNA object for LiveSeq

Package variables

Included modules

Inherit

Bio::LiveSeq::SeqI

Synopsis

  # documentation needed

Description

This holds the DNA sequence (or the RNA in the case of cDNA entries)
and is accessed by exons, genes, transcripts... objects

Methods

Methods description

  Title   : new
  Usage   : $dna = Bio::LiveSeq::DNA->new(-seq => "atcgaccaatggacctca",
					  -offset => 3 );

  Function: generates a new Bio::LiveSeq::DNA
  Returns : reference to a new object of class DNA
  Errorcode -1
  Args    : a string
        AND an optional offset to create nucleotide labels (default is 1, i.e.
            starting the count of labels from "1") -> do not bother using it ->
            it could be used by alternative loaders !EMBL format
  NOTE    : strand of DNA is set to 1 by default

Methods code

sub length {

  my $self=shift;
  return $self->chain_length();
}

# it is overridden to provide MUCH faster output

}

sub new {

  my ($thing, %args) = @_;
  my $class = ref($thing) || $thing;
  my (%empty,$obj);

  if ($args{-seq}) {
    $obj = $thing->string2chain($args{-seq},$args{-offset}); # inherited from ChainI
    $obj = bless $obj, $class;
  } else {
    $obj=\%empty;
    $obj = bless $obj, $class;
    $obj->throw("$class not initialized properly");
  }

  $obj->{'alphabet'}='dna'; # set alphabet default
  $obj->{'strand'}=1; # set strand default = 1
  $obj->{'seq'}=$obj; # set seq field to itself

  return $obj;
}

# START method
# it has to be redefined here because default from SeqI accesses field "start"

}

sub start {

  my $self = shift;
  return $self->{'begin'}; # the chain's start is called begin
}

# it is overridden to provide faster output

}

sub valid {

  my $self=shift(@_);
  return $self->label_exists(@_);
}

1;

}

General documentation

Email: Insana@ebi.ac.uk, jinsana@gmx.net
Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _